When analyzing samples with an analytical instrument, such as a mass spectrometer that has a matrix assisted laser desorption/ionization (MALDI) ion source, the samples are commonly mixed into in a UV absorbing matrix material and then deposited on a sample plate where the sample and matrix co-crystallize upon drying. A focused pulse of UV energy from a laser beam is directed at the sample, and the UV energy ionizes the sample, which is then passed from the ion source to the analytical instrument through a small orifice such as that defined by a capillary tube. For accurate analysis, the laser beam spot must impinge the plate in a location coinciding with the center axis of the orifice opening of the instrument. Any deviation (even as low as a few hundred microns) from this location of impingement is detrimental to the sensitivity of the spectrometer.
Alignment is commonly attempted using a video camera to image the laser beam spot and the proximal end of the orifice opening. Due to a parallax effect, however, it can be difficult to accurately align the laser beam spot.